3NDJ

X-ray Structure of a C-3'-Methyltransferase in Complex with S-Adenosyl-L-Homocysteine and Sugar Product


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherIn-house MIR model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82981.3 M - 1.5 M Sodium/potassium phosphate, 10 mM dTMP, 5 mM S-adenosyl-L-homocysteine. , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3748.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.944α = 90
b = 114.447β = 90
c = 37.825γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135Montel2010-04-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.457.297.40.0720.07211.094.218704784778
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.5940.2540.2542.62.4214813

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTIn-house MIR model1.5206988366407347698.190.2050.204990.203140.23973RANDOM10.98
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.180.150.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.236
r_dihedral_angle_4_deg18.017
r_dihedral_angle_3_deg14.036
r_dihedral_angle_1_deg6.212
r_scangle_it4.99
r_scbond_it3.493
r_mcangle_it2.321
r_angle_refined_deg2.222
r_mcbond_it1.656
r_chiral_restr0.152
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.236
r_dihedral_angle_4_deg18.017
r_dihedral_angle_3_deg14.036
r_dihedral_angle_1_deg6.212
r_scangle_it4.99
r_scbond_it3.493
r_mcangle_it2.321
r_angle_refined_deg2.222
r_mcbond_it1.656
r_chiral_restr0.152
r_bond_refined_d0.012
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3162
Nucleic Acid Atoms
Solvent Atoms408
Heterogen Atoms67

Software

Software
Software NamePurpose
PROTEUM PLUSdata collection
PHASERphasing
REFMACrefinement
SAINTdata reduction
SADABSdata scaling